Forensic anthropologist Temperance "Bones" Brennan and her team work with the FBI to solve murders by identifying victims from their remains in a procedural series inspired by real-life forensic anthropologist and novelist Kathy Reichs.
Booth goes missing as Season 11 begins six months after he and Brennan left their careers behind, but a case with ties to the couple pulls Brennan back into the world of forensic analysis, which brings her into contact with a member of Booth's family and Arastoo Vaziri, who's taken the lead at the Jeffersonian in her absence. Meanwhile, the FBI investigate Booth's disappearance, but one agent's tactics are bad for the team's morale.
Booth is still missing, but the team learns that Agent Miller has hidden information about his whereabouts and physical state. Meanwhile, a digital forensic scientist helps Angela try to decipher information pertaining to Booth's location and the circumstances of his disappearance; and Arastoo makes a decision that will change his and Cam's personal and professional relationships.
Remains found at a fish farm coincide with Brennan and Booth returning to their jobs at the Jeffersonian and the FBI, respectively, and it's revealed that some of the victim's organs were harvested before he was dumped in the water. Meanwhile, Hodgins urges Angela to exhibit her photographs; Cam deals with her decision to choose work over romance; and Booth finds Aubrey in his old office.
A real-estate agent's remains are discovered in a forest and show signs of being partially devoured by coyote-wolf hybrids, so Brennan solicits help from an older, distinguished forensic anthropologist, who amazes the staff with her decades of experience and surprising knowledge of fantasy football, with which the victim was heavily involved and even linked him to a social-media feud with an NFL star.
A case involving a 200-year-old headless corpse gets some help from Ichabod Crane and FBI agent Abbie Mills, who travel from Sleepy Hollow to claim the body, but wonder what it has to do with a contemporary murder victim. Meanwhile, Brennan and Booth surprise each other with Halloween pranks.
The body of a U.S. senator is found in a street sweeper by an unusual pair of sanitation workers. Meanwhile, Aubrey pursues a relationship with "squintern" Jessica, but he also secretly digs into her past to make sure there are no skeletons in her closet that could ruin his dreams of a political future.
An escape artist's body is found in the woods, and it's revealed that he may have had enemies in the magic community. Meanwhile, Brennan and Booth ask their friends to opine on their tooth-fairy debate; and Angela continues to work on her photography with Sebastian Kohl.
A political journalist is found dead after writing an article exposing corruption at the NSA, and Hodgins becomes paranoid when he's convinced their investigation is being closely monitored. Meanwhile, the team gathers for Thanksgiving; and Brennan plans a surprise for Booth.
Hodgins' rehab continues eight weeks after the explosion that left him paralyzed, but he's not quite ready to accept spending the rest of his life in a wheelchair. Meanwhile, Brennan and Booth investigate the death of a public defender whose long list of clients reveals plenty of murder suspects.
A body found in a car crash is identified as a leader of an organization that promotes men's rights, but the investigation leads to an intense clash between Brennan and the deceased's cofounder. Meanwhile, Hodgins' bitterness creates dilemmas for Angela and the staff; and Booth thinks his wife is a jinx for his beloved Philadelphia Flyers hockey team.
A social worker's remains are found, but evidence suggests the victim had been dead for months before the body was dumped in a park, and the case gets even more twisted when it's linked to a serial killer known for desecrating corpses. Meanwhile, Booth and Aubrey hope a behavioral analyst can provide some clues about the murderer; and Cam tries to sort out her romantic life.
The murder of an ex-con who was living in a halfway house, but vanished, is investigated, and a suspect is linked to Booth. Meanwhile, Brennan is called to testify about her assault of an unarmed individual during a past case, which could result in a suspension; Aubrey and Jessica miss another chance for a first kiss; and the rift widens between Hodgins and Angela.
A private investigator's body is found frozen in ice after being thrown in the Potomac, and the investigation reveals that the victim was a fixer who had a long list of enemies. Meanwhile, Aubrey learns shocking information about his father; Brennan and Booth get Christine's first report card; and Karen Delfs asks Aubrey if he wants to go on a date.
A body found in a rat lab at Lynwood University turns out to be the head of a male a cappella group who recently ejected one of their best singers. Meanwhile, Booth hopes to go on a summer vacation with Parker; a new intern joins the Jeffersonian; and Aubrey's college experience becomes a topic of interest.
A Secret Service agent's body is discovered by an inebriated college student on the eve of a presidential visit, but Booth is blindsided when the agency refuses his help with the case. Meanwhile, Brennan won't let the flu keep her from work even though Dr. Colin Fisher has returned to the Jeffersonian to lead the investigation; and Hodgins attempts a risky experiment to change his life.
As part of a promotion for the Jeffersonian's Medico-Legal lab, a film crew follows the team as they investigate a murder case involving a corpse buried in a landfill more than 10 years ago, and each member provides commentary in their fields of expertise.
The death of a professional hockey player is investigated after his headless corpse is found in a river, and Booth's love of the sport proves to be an asset in the case, but it also reunites him with an old rival and puts him back on the ice. Meanwhile, Hodgins and Oliver compete to build a drone to retrieve the victim's head; and Brennan and Booth try to get their home organized and free of clutter.
A billionaire explorer's remains are discovered in Antarctica 10 years after he disappeared, but the Jeffersonian's Dr. Clark Edison winds up on a list of murder suspects since he was a member of the expedition. Meanwhile, Cam clashes with her sister when she arrives in town to help with her wedding plans.
A corpse at a glass recycling plant has a diamond stuck in its jaw, and Inspector Rousseau suspects a descendant of French nobility—who turns out to be the victim's husband—may have had something to do with the murder. Meanwhile, Booth learns he has an eye ailment; and Hodgins thinks a ghost is following him.
In the Season 11 finale, the search for the Puppeteer, a serial killer who turns his victims into marionettes, continues, but Brennan can't shake her guilt of failing to catch the perpetrator due to her brief period of retirement.